Discoveries have revealed the multifactorial roles oligonucleotides play in vitro and in vivo. It has been demonstrated, that oligonucleotides can act as catalysts (ribozymes and DNAzymes) (J. Doudna and T. Cech, Nature 2002, 418, 222; S. Santoro and G. Joyce, Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 4262), sensors (aptamers) (R. Breaker, Curr. Opin. Biotechnol. 2002, 13, 31), gene expression platforms (riboswitches and antiswitches) (R. Breaker, Nature 2004, 432, 838; M. Mandal and R. Breaker, Nat. Rev. Mol. Cell. Biol. 2004, 5, 451; T. Bayer and C. Smolke, C. D., Nat. Biotechnol. 2005, 23, 337), and gene regulatory elements (antisense DNA, siRNA, and miRNA) (L. Scherer et al., Nat. Biotechnol. 2003, 21, 1457; A. Fire et al., Nature 1998, 391, 806).
In order to study the function of oligonucleotides in a detailed fashion and to employ oligonucleotides as highly specific biological research tools, precise control over their activity in a spatial and a temporal manner is required. In this context, light represents an ideal control element since it can be precisely controlled in amplitude, location, and timing thus imposing spatio-temporal control on the system under study (D. Young and A. Deiters, Org. Biomol. Chem. 2007, 5, 999; X. Tang and I. Dmochowski, Mol. BioSyst. 2007, 3, 100; M. Goeldner and R. Givens, Dynamic Studies in Biology: Phototriggers, Photoswitches and Caged Biomolecules. Wiley-VCH: Weinheim, 2005; p xxvii; G. Mayer and A. Heckel, Angew. Chem. Int. Ed 2006, 45, 4900; G. Dorman and G. Prestwich, Trends Biotechnol. 2000, 18, 64; D. Lawrence, Curr. Opin. Chem. Biol. 2005, 9, 570). The most common technique of conveying light-regulation to biological processes involves the installation of a photo-protecting group on a biologically active molecule which can be completely removed via light irradiation. This process, termed ‘caging’, has been successfully employed to the light-controlled activation of small molecule inducers of gene expression, fluorophores, peptides, and proteins (Id). DNA and RNA have been caged as well, mostly through statistical reaction of the phosphate backbone of the synthesized or transcribed oligonucleotide with reactive diazo-derivatives of caging groups (S. Shah et al., Angew. Chem. Int. Ed. Engl. 2005, 44, 1328; H. Ando et al., Nat. Genet. 2001, 28, 317). The major disadvantage of this approach is that no control over the position and number of installed caging groups can be achieved. Moreover, caging groups are only installed on the phosphate backbone, not on the heterocyclic base itself, failing to disrupt Watson-Crick base pairing. Recently, approaches to the site-specific caging of DNA have been reported. The introduction of an 0-4 caged thymidine has been successfully applied to the photochemical activation of transcription and aptamer binding (L. Krock and A. Heckel, Angew. Chem. Int. Ed. 2005, 44, 471; A. Heckel and G. Mayer, J. Am. Chem. Soc. 2005, 127, 822). However, due to the lability of the caging group special DNA synthesis conditions were necessary. An adenosine modified with a sterically demanding, photo-removable imidazolylethylthio group has been used to photochemically activate an 8-17E DNAzyme (R. Ting et al., J. Am. Chem. Soc. 2004, 126, 12720). After irradiation for 8-10 min with short-wavelength UV light (254-310 nm) only 30% of RNA cleavage was observed after a 60 min reaction time. Since the caging group was installed at C-8, no hydrogen bonding of the adenosine was disrupted. Reversible switching of DNAzyme activity was previously achieved through incorporation of diazobenzene motifs, however, only a 5- to 9-fold rate modulation upon irradiation was obtained (Y. Liu and D. Sen. J. Mol. Biol. 2004, 341, 887; S. Keiper and J. Vyle, Angew. Chem. Int. Ed. Engl. 2006, 45, 3306).